[maker-devel] Maker quesiton

[Jeff Maughan]

Carson,

Thanks for the quick reply!  Worked perfectly!

Jeff

From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Wednesday, April 29, 2015 at 1:39 PM
To: Peter J Maughan <Jeff_Maughan at byu.edu<mailto:Jeff_Maughan at byu.edu>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Maker quesiton

Hi Jeff,

The structure of GFF3 files, means they cannot be concatenated. You can merge them by using the gff3_merge tool and giving it multiple GFF3 files (see usage statement).  It will take care of pulling them apart, reordering things, and then putting them back together in a usable way.

-Carson



On Apr 28, 2015, at 5:58 PM, Jeff Maughan <jeff_maughan at byu.edu<mailto:jeff_maughan at byu.edu>> wrote:

Hi!

I have a genome that is about 400 Mb.  I couldn't get MPI to run on our server, so I just divided up the genome into 10Mb chucks and ran them separately.  Worked great (about 40 jobs).  I used fasta_merge and gff_merge on each of the subsets.  I thought I would then just concatenate (cat) each of the 40 files together and then I would be able to use maker_map_ids (etc.) and maker_functional_gff (etc) to rename and add function.  Unfortunately it seems to only map the ids for the first subset in the concatenated file...

Any ideas?  Is there another way to merge these files together so they play nice with the downstream scripts.

Thanks,

Jeff Maughan

PS I'm obviously not a trained bioinformaticist.

P. Jeff Maughan, Ph.D. | Professor | Department of Plant and Wildlife Sciences
701 East University Parkway Drive
5144 LSB, Provo, Utah, 84602 | Brigham Young University
http://lifesciences.byu.edu/~pjm43
http://orphanedcrops.byu.edu/
*: Jeff_Maughan at byu.edu<mailto:Jeff_Maughan at byu.edu>
*: (801) 422-8698




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